ENST00000420000.6:n.537+3200C>A

Variant names:

• chr3-3334100-G-T
• rs9835812
• ENST00000420000.6:n.537+3200C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):​n.537+3200C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,156 control chromosomes in the GnomAD database, including 1,513 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.081 (1513 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223727	ENST00000420000.6	n.537+3200C>A		intron_variant	Intron 4 of 4	4
ENSG00000223727	ENST00000451031.5	n.339+3200C>A		intron_variant	Intron 3 of 5	3
ENSG00000223727	ENST00000455703.1	n.396+3200C>A		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12272 AN: 152038 Hom.: 1506 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00116

Gnomad OTH AF: 0.0632

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0809 AC: 12304 AN: 152156 Hom.: 1513 Cov.: 32 AF XY: 0.0783 AC XY: 5826 AN XY: 74412

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00116

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0107 Hom.: 227

Bravo AF: 0.0910

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9835812; hg19: chr3-3375784;